scRecover

DOI: 10.18129/B9.bioc.scRecover    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see scRecover.

scRecover for imputation of single-cell RNA-seq data

Bioconductor version: 3.13

scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.

Author: Zhun Miao, Xuegong Zhang <zhangxg at tsinghua.edu.cn>

Maintainer: Zhun Miao <miaoz13 at tsinghua.org.cn>

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scRecover")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scRecover")

 

HTML	R Script	scRecover
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.9 (R-3.6) (2.5 years)
License	GPL
Depends	R (>= 3.4.0)
Imports	stats, utils, methods, graphics, doParallel, foreach, parallel, penalized, kernlab, rsvd, Matrix (>= 1.2-14), MASS (>= 7.3-45), pscl (>= 1.4.9), bbmle (>= 1.0.18), gamlss (>= 4.4-0), preseqR (>= 4.0.0), SAVER (>= 1.1.1), Rmagic (>= 1.3.0), BiocParallel(>= 1.12.0)
LinkingTo
Suggests	knitr, rmarkdown, SingleCellExperiment, testthat
SystemRequirements
Enhances
URL	https://miaozhun.github.io/scRecover
BugReports	https://github.com/miaozhun/scRecover/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	scRecover_1.8.0.tar.gz
Windows Binary	scRecover_1.8.0.zip
macOS 10.13 (High Sierra)	scRecover_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scRecover
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scRecover
Package Short Url	https://bioconductor.org/packages/scRecover/
Package Downloads Report	Download Stats